The INCF Neuroinformatics blog
Professor, researcher, neuroscientist and author, David Willshaw talks to INCF about his research, projects and achievements.
NCF: Can you give us some background information about yourself?
Willshaw: I'm Professor of Computational Neurobiology at the University of Edinburgh, UK. My research has focused on neural networks and computational neuroscience, stretching back over 40 years. I've also developed algorithms for combinatorial optimization. Since 1984, I've held long term research support from the UK Medical Research Council and, more recently, the Wellcome Trust. Currently I lead a multi-centre Wellcome Trust funded project combining modelling approaches to investigate the roles of neural activity and molecular signalling in the formation of ordered nerve connections in the mouse retinocollicular system.
I'm the grant holder of the Edinburgh Doctoral Training Centre in Neuroinformatics and Computational Neuroscience. Since 2002, this Centre has trained over 80 PhD students from the physical and informational sciences who are applying quantitative approaches to neuroscience and to neurally inspired computing.
From 1999-2005, I was Editor-in-Chief of the computational neuroscience journal Network: Computation in Neural Systems. With colleagues, in 2012 I published the textbook Principles of Computational Modelling in Neuroscience (Cambridge University Press; 2011).
Since 2001, I have coordinated Neuroinformatics research in the UK.
Currently, I am the UK Node Coordinator and Scientific Representative to INCF. I’ve a special interest in training and now chair the INCF Training Committee. In our first full year of operation, last year we funded three short courses in particular aspects of Neuroinformatics and also ran our own introductory short course.
INCF: When did you become interested in Neuroinformatics?
Willshaw: I've been interested in applying computational modelling techniques to understanding the brain ever since I read books on information theory and cybernetics as a teenager and was then inspired at university by lectures on the neurobiology of vision.
INCF: What is a normal day in the life of a Neuroinformatics researcher?
Willshaw: A combination of meetings about projects and new initiatives plus too little time for research. My most fruitful time to do research is when I’m away from the office; the Elastic Net algorithm for the Travelling Salesman Problem which I developed with Richard Durbin was essentially worked out whilst we were attending a summer school.
INCF: Some highlights from 2012...
Willshaw: I've been analyzing some new imaging data, which gives insights about how the connectivity pattern between the eye and the brain is set up. After spending many hours analyzing the data in the wrong way, finally I succeeded. As a modeller I’m proud of the fact that the results of the analysis are inexplicable on any current model!
INCF: Some projects for 2013...
Willshaw: To get my analysis published and to make sure the UK Node stays on a firm footing.
Dr Upinder Bhalla, member of the INCF India Node, National Centre for Biological Sciences Bangalore, India, talks about his life as neuroinformatics researcher, projects and interests.
INCF: Tell us a little about your background.
Bhalla: I started out keenly interested in science, convinced I would do physics. An undergraduate biology course at Cambridge was a revelation, so I switched subjects for my PhD. I worked on the GENESIS neuronal simulator as a grad student at Caltech in the group of Jim Bower, and then adapted it to carry out kinetic simulations as a post-doc in Mount Sinai with Ravi Iyengar. I've combined experiments and models on studying olfactory processing, and memory, ever since. I now work on the MOOSE simulator which brings together many scales of function, from molecules to vast networks, that I am convinced are essential to consider to understand neuronal function.
INCF: When did you become interested in Neuroinformatics?
Bhalla: As a grad student, doing neuronal modeling and development of GENESIS. I had an interesting meeting with Mike Hines back then thinking how we could get GENESIS and NEURON to talk to each other. Still trying to achieve interoperability!
INCF: How is a regular day in the life of a neuroinformatics researcher ?
Bhalla: Cycle in, swim, deal with email, deal with committees, prepare a lecture or grant, do some science with students if possible. Cycle back, get down to quality science time in the evening when the kids have gone to sleep. Unfortunately brain switches off about the same time.
INCF: Some highlights from 2012...
Bhalla: Watching Olympics at midnight. Enjoying wandering about lost in Munich at the INCF Congress. Seeing our lab's first 2-photon in-vivo activity recordings from a whole sheet of pyramidal neurons.
INCF: Projects for 2013...
Bhalla: MOOSE with lots of new features and parallelism. Graduate a lot of students. Multiscale models in hippocampal plasticity.
INCF: Last book you have read...
Bhalla: Anathem by Neal Stephenson.
INCF: Last movie you have seen...
Bhalla: English Vinglish (2012, directed by Gauri Shinde)
INCF: What is your secret hobby?
Bhalla: Eat vast amounts of dessert to annoy colleagues who have to watch their weight. But this isn't secret any more!
The Society for Neuroscience celebrated its annual meeting from 14 to 18th October, in New Orleans, US. As in previous years, INCF offered a series of dual demo sessions of Neuroinformatics tools and software (short demo videos are available on the INCF YouTube Channel). An open mini-hackathon took place on Wednesday, were developers were welcome to join for on-site coding and discussion. The INCF DATASPACE was launched during SfN, along with the Data Share Award. INCF was located near other Neuroinformatics exhibitors like Neuroscience Information Framework (NIF), Whole Brain Catalogue, Cognitive Atlas, CARMEN and NeuroDevian.
The 5th Annual INCF Congress of Neuroinformatics took place September 10-12 at the University Hospital Klinikum rechts der Isar der TU München, in Munich, Germany. It welcomed more than 200 researchers in all fields related to neuroinformatics, including data- and knowledge-bases of the nervous system from molecular to behavioral levels; tools for the acquisition, analysis, and visualization of nervous system data; and theoretical, computational, and simulation environments for modeling the brain. The meeting included a series of keynote speakers, workshops, poster sessions and live demonstrations of neuroinformatics tools.
Dr. Sean Hill, Executive Director of the International Neuroinformatics Coordinating Facility –INCF- explains: “The Annual INCF Neuroinformatics Congress brings together world class scientists and a diverse international research community to exchange tools, techniques and knowledge for the acceleration of our understanding of the brain through data sharing and multilevel analysis, data integration and computational modeling“.
Some highlights of the event included:
- Keynote speakers: Michael Brecht, Sonia Grün, Atushi Miyawaki, Russel Poldrack and Gordon Shepherd.
- On Sunday September 10th, Yasuo Kawaguchi, Carl Petersen, and Harald Luksch presented their work in a workshop on the “Function-structure relationship in microcircuitry.”
- On Monday September 11th, Kim “Avrama” Blackwell, Thomas Bartol, Nicolas Le Novère, and Upinder Bhalla presented in a workshop on the “Systems Biology of the Neuron.”
- On Wednesday September 12th, Cameron Neylon, Amarnath Gupta, and Mercè Crosas participated in a workshop on “If there is a data deluge, where are the data?”
Immediately following Neuroinformatics 2012, the same venue hosted the Bernstein Conference on Computational Neuroscience, the annual meeting of the National Bernstein Network Computational Neuroscience (NNCN) that represents about 200 research groups from over 20 locations in Germany.
A full program and further information is available at the website: neuroinformatics2012.org
The meeting was sponsored by: Bernstein Network, IEEE-EMB, CARMEN, Springer and Columbia University Press and Physion Consulting.
One of the high points of our year is taking part in the overwhelming array of new exciting neuroscience at SfN.
As in previous years, the INCF exhibit booth at the annual SfN meeting was well attended. Our co-location (see map) with other neuroinformatics projects and initiatives helps - visitors interested in our activities are likely interested in our booth neighbors, and vice versa - and probably also our hosted program of live neuroinformatics demos. (Though we suspect that our comfy sofa might also be a contributing factor.)
This year we added a satellite workshop to our schedule, "Neuroshare revisited" on November 12, for a discussion on the state of Neuroshare and possible future developments to the format in order to improve and facilitate access to neurophysiological data. It was organized through the INCF Program on Standards for Datasharing, and we invited data acquisition system vendors, data analysis software developers, and users to talk about needs and problems - it turned out to be a very interesting discussion. The group agreed that extending Neuroshare would be a worthwhile endeavor.
We devoted a full day of our neuroinformatics demo program to digital brain atlasing. Representatives from the INCF Program on Digital Brain Atlasing held a "Walk-in Registration Clinic" for researchers with rodent data and an interest in sharing them through the Program's infrastructure. We were even visited by George Paxinos (yes, that Paxinos)!
Our other two scientific programs were also represented - the Program on Ontologies of Neural Structures through the "Adopt a Neuron" campaign which was also presented in our booth during a demo, and the Program on Multiscale Modeling through a demo of a reference implementation in progress for NineML (the Network Interchange for Neuroscience ML). And there were many other interesting demo contributions from Programs, Nodes and the scientific community - you can see them all here.
This dazzling array of new information - posters, lectures, exhibitors and a constant flow of brief tweeted updates - and many interactions with scientific community from all over the world is what makes the SfN week one of the high points of our year, and this year was no exception. Unfortunately, there is never any way to see all that is potentially interesting at SfN. But some key lectures have been saved for posterity in video format on SfN's YouTube channel - for instance the Kavli minisymposium on legal implications of neuroscience advances.
The Congress itself takes place September 4-6. But there are also other events planned before and after the main meeting.
We have just made the 2011 Abstract book, with abstracts for all keynotes, workshops, demos and posters, available as a pdf for browsing and download (including a handy clickable index at the end!)
Satellite Workshop on September 3
The Congress kicks off already September 3 with the satellite workshop "Toward a Global Neuroinformatics Infrastructure" organized in collaboration with the IEEE Engineering in Medicine and Biology Society at their yearly meeting EMBC, held at the Boston Marriott Copley Place Hotel. The workshop will include presentations from the leaders of large neuroscience infrastructure projects from around the world:
Main meeting September 4-6
The main meeting will feature 5 keynote lectures, 8 spotlight presentations of selected demos and posters, 12 workshop speakers, 35 demos and and 130 posters, as well as the INCF US Node Special Symposium (with another 9 lectures) on the afternoon of the last meeting day, September 6. The same day, September 6, also offers lunch seminars sponsored by BIRN. All details can be found on the meeting web pages.
INCF Task Force meetings September 7-8
Taking advantage of the fact that a large part of our community is present in Boston, after the main meeting we are also organizing meetings for many of the Task Forces associated with the INCF Scientific Programs, including a cross-Task Force hackathon at MIT on September 8.
The 20th conference of the Organisation for Computational Neurosciences (OCNS) takes place in Stockholm, July 23-28 - and INCF is there.
We can now, based on empirical testing in the form of the CNS*2011 reception, conclude that the Stockholm City Hall is just about a comfortable fit for some five hundred mingling conference attendees - where they fit the additional eight hundred people at the 1300-guest Nobel banquet will remain a mystery.
CNS*2011 attendees in the Stockholm City Hall's Golden Hall.
One of the high points of the CNS*2011 meeting are the poster sessions - this year, almost four hundred posters were presented in three intense poster sessions.
Among the work presented we found one of the first posters produced from the EuroSPIN Erasmus Mundus program, which offers joint doctoral degrees in neuroinformatics and is offered by a consortium consisting of four universities in INCF member countries: National Centre for Biological Science, Bangalore, India; University of Edinburgh, UK; Albert Ludwig University of Freiburg, Germany, and KTH in Sweden . We also found a poster on CoCoMac 2.0, a macaque brain atlas with an interface built on the INCF Scalable Brain Atlas.
Left: Oliver Muthmann, EuroSPIN PhD student, and Jeanette Hellgren Kotaleski, EuroSPIN Program Coordinator. Right: Rembrandt Bakker, explaining the CoCoMac 2.0 poster to Hermann Cuntz.
For the INCF Multiscale Modeling program, one of the most important events at CNS*2011 was the workshop Emerging standards in network modeling, which served as an update on the state of the art in the field, as well as the release of the initial version of the model description language NineML. Documentation and tutorials for NineML can be found at the INCF Software Center NineML pages.
This summer, you can meet INCF at a number of conferences: HBM in Quebec, IBRO in Florence, CNS in Stockholm, and our own Neuroinformatics Congress in Boston.
This Saturday, June 25, our summer conference season starts in earnest, with our satellite workshop on Neuroimaging Data Sharing and Data Access in Quebec, just before the launch of HBM*2011. The workshop has been greeted with much interest and is full - close to 100 attendees - with a waiting list. The following week, June 26-30, we will be present as exhibitors at HBM*2011, in booth 104.
Two weeks later, July 14-18, we will exhibit at the 8th IBRO World Congress of Neuroscience in Florence. Since we have recently become a member of IBRO, we are looking forward to meeting the IBRO community. Come meet us in booth 35!
Less than a week after IBRO, the CNS*2011 conference opens its doors in our hometown Stockholm. We have an exhibitor table, we are organizing a workshop on Emerging standards in network modeling on July 27, and we are also one of the local co-organizers - you'll meet us in various places during the conference days July 23-28.
After these three events, it is a month to go to the great finale - our own Neuroinformatics Congress in Boston, September 4-6. We are actually starting a day early, September 3, with a workshop during the last day of the EMBC conference; Toward a Global Neuroinformatics Infrastructure which includes talks by four world leaders of neuroinformatics and a concluding panel discussion. The registration fee for this last day of EMBC will be significantly discounted for Neuroinformatics Congress attendees.
And then? We start looking forward to meeting you all at SfN*2011 in Washington DC in November, of course.
On May 10-11, representatives from the INCF National Nodes met in Stockholm for the Nodes Workshop.
Last week, 33 representatives from 14 of the 16 INCF National Nodes met in Stockholm for the fourth Nodes Workshop. This meeting's theme was "Neuroinformatics Infrastructure". The INCF Secretariat presented its visions for global neuroinformatics infrastructure, and each Node was asked to give a brief overview of their country's current neuroscience infrastructure status. Breakout discussion sessions collected input and ideas on data sharing, infrastructure needs, and teaching and training aspects of neuroinformatics.
As usual, the meeting also afforded plenty of opportunities for discussion and networking between the participants - over coffee, during the poster session and at lunch and dinner. We look forward to meeting you all again next time!
INCF now has a blog! Follow us via RSS or visit each week to keep track of INCF activities and neuroinformatics news, tools & resources and events.
This is the inaugural post of the new INCF blog, where we plan to highlight neuroinformatics news, events and resources - big and small. If there is something you would like to see featured or discussed here, you are very welcome to contact us on email@example.com with your feedback.